ENST00000660486.1:n.50+5715T>C

Variant names:

• chr11-111019216-T-C
• rs11213703
• ENST00000660486.1:n.50+5715T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000660486.1(ENSG00000287556):​n.50+5715T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.377 in 152,090 control chromosomes in the GnomAD database, including 11,528 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.38 (11528 hom., cov: 33)
• Consequence: ENSG00000287556 ENST00000660486.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0490
• Publications: 4 publications found

Genes affected

ENSG00000287556 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.767 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369489	XR_948009.2	n.1278-558A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287556	ENST00000660486.1	n.50+5715T>C		intron_variant	Intron 1 of 1
ENSG00000299094	ENST00000760419.1	n.198-558A>G		intron_variant	Intron 1 of 2
ENSG00000299094	ENST00000760420.1	n.395+210A>G		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.377 AC: 57241 AN: 151972 Hom.: 11512 Cov.: 33

Gnomad AFR AF: 0.391

Gnomad AMI AF: 0.262

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.434

Gnomad EAS AF: 0.788

Gnomad SAS AF: 0.658

Gnomad FIN AF: 0.327

Gnomad MID AF: 0.471

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.382

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.377 AC: 57297 AN: 152090 Hom.: 11528 Cov.: 33 AF XY: 0.387 AC XY: 28755 AN XY: 74338

African (AFR) AF: 0.391 AC: 16211 AN: 41466

American (AMR) AF: 0.395 AC: 6035 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.434 AC: 1505 AN: 3468

East Asian (EAS) AF: 0.787 AC: 4080 AN: 5182

South Asian (SAS) AF: 0.658 AC: 3170 AN: 4820

European-Finnish (FIN) AF: 0.327 AC: 3457 AN: 10584

Middle Eastern (MID) AF: 0.493 AC: 144 AN: 292

European-Non Finnish (NFE) AF: 0.318 AC: 21638 AN: 67968

Other (OTH) AF: 0.388 AC: 819 AN: 2112

Alfa AF: 0.358 Hom.: 8433

Bravo AF: 0.380

Asia WGS AF: 0.690 AC: 2397 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	5.2
DANN	Benign	0.48
PhyloP100		-0.049

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs11213703; hg19: chr11-110889940;